You're reasoning strikes me as very unsound. The fact Ms has a huge case with a huge fan implies they can deal with more heat than PS4, no? Ergo the possibility that MS can upclock but Sony can't.
Assuming yield concerns have been satisfied:
Adjusting noise margins and airflow limits might buy margin for both without changing the physical design of the box and cooler.
I'm curious how closely specced the power supplies are to the silicon.
One difference is that the PS4's internal power supply does imply the cooling apparatus and the box itself have a stronger physical reason to be sized to the whole console's power target, and changes here past a certain point may lead to impacts on the power supply, cooler, and case because of the physical integration.
There could be more leeway with the separate power supply on the Xbox One to vary things because there are fewer potential knock-on effects to deciding on a somewhat higher total power target.
However, if the upclock comes in due to improved manufacturing leading to better performance iso-power, this may not be something they need to worry about. It also might be something the competing design could try for. This is something that would be dependent on specific details of the actual physical implementation and manufacturing trends.
How about a day-one firmware patch from both that sets the final clocks they pick the day before release, for maximum levity?